PDBe-KB: collaboratively defining the biological context of structural data

PDBe-KB consortium

doi:10.1093/nar/gkab988

PDBe-KB: collaboratively defining the biological context of structural data

PDBe-KB consortium

Research output: Contribution to journal › Article › peer-review

50 Citations (Scopus)

26 Downloads (Pure)

Abstract

The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.

Original language	English
Pages (from-to)	D534-D542
Number of pages	9
Journal	Nucleic Acids Research
Volume	50
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkab988
Publication status	Published - 7 Jan 2022

Bibliographical note

Funding Information:
ELIXIR [IDP implementation study]; Biotechnology and Biological Sciences Research Council via the 3D-Gateway [BB/T01959X/1]; FunPDBe [BB/P024351/1]; European Molecular Biology Laboratory-European Bioinformatics Institute who supported this work; J.D. acknowledges support from the Ministry of Education, Youth and Sport of the Czech Republic [INBIO CZ.02.1.01/0.0/0.0/16 026/0008451]; R.S., K.B. and J.D. also acknowledge support from the Ministry of Education, Youth and Sport of the Czech Republic [ELIXIR-CZ LM2018131]; L.M. acknowledges support from the European Union’s Horizon 2020 Programme (H2020-INFRAIA-2018-1) [823839]; Research Founda- tion Flanders (FWO) [G032816N, G042518N, G028821N]; W.V. acknowledges support from the Research Foundation Flanders (FWO) [G032816N, G028821N]; A.R. acknowledges support from the Fondazione Cassa Di Risparmio di Firenze [24316]; European Commission [101017567]; M.H.C. acknowledges the AIRC project to MHC [IG 23539]; J.F.-R. acknowledges support from the Spanish Ministry of Science and Innovation [PID2019-110167RB-I00]; N.R. acknowledges support from the Norwegian Research Council (Norges Forskningsråd) [288008]; E.D.L. acknowledges support from the European Union’s Horizon 2020 research and innovation programme [819318]; M.J.E.S. acknowledges support from the Wellcome Trust [104955/Z/14/Z, 218242/Z/19/Z]. Funding for open access charge: Biotechnology and Biological Sciences Research Council grant [BB/T01959X/1]; Wellcome Trust [104955/Z/14/Z and 218242/Z/19/Z]. Conflict of interest statement. None declared.

Publisher Copyright:
© The Author(s) 2021.

Copyright:
Copyright 2022 Elsevier B.V., All rights reserved.

Access to Document

10.1093/nar/gkab988Licence: CC BY

81668276Final published version, 1.63 MBLicence: CC BY

Cite this

@article{e23d72329dcd4b8bb334c82b254996a2,

title = "PDBe-KB: collaboratively defining the biological context of structural data",

abstract = "The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.",

author = "{PDBe-KB consortium} and Mihaly Varadi and Stephen Anyango and David Armstrong and John Berrisford and Preeti Choudhary and Mandar Deshpande and Nurul Nadzirin and Nair, {Sreenath S.} and Lukas Pravda and Ahsan Tanweer and Bissan Al-Lazikani and Claudia Andreini and Barton, {Geoffrey J.} and David Bednar and Karel Berka and Tom Blundell and Brock, {Kelly P.} and {Maria Carazo}, Jose and Jiri Damborsky and Alessia David and Sucharita Dey and Roland Dunbrack and {Fernandez Recio}, Juan and Franca Fraternali and Toby Gibson and Manuela Helmer-Citterich and David Hoksza and Thomas Hopf and David Jakubec and Natarajan Kannan and Radoslav Krivak and Manjeet Kumar and Levy, {Emmanuel D.} and Nir London and Macias, {Jose Ramon} and Srivatsan, {Madhusudhan M.} and Marks, {Debora S.} and Lennart Martens and McGowan, {Stuart A.} and McGreig, {Jake E.} and Vivek Modi and {Gonzalo Parra}, R. and Gerardo Pepe and Damiano Piovesan and Jaime Prilusky and Valeria Putignano and Radusky, {Leandro G.} and Pathmanaban Ramasamy and Rausch, {Atilio O.} and Wim Vranken",

note = "Funding Information: ELIXIR [IDP implementation study]; Biotechnology and Biological Sciences Research Council via the 3D-Gateway [BB/T01959X/1]; FunPDBe [BB/P024351/1]; European Molecular Biology Laboratory-European Bioinformatics Institute who supported this work; J.D. acknowledges support from the Ministry of Education, Youth and Sport of the Czech Republic [INBIO CZ.02.1.01/0.0/0.0/16 026/0008451]; R.S., K.B. and J.D. also acknowledge support from the Ministry of Education, Youth and Sport of the Czech Republic [ELIXIR-CZ LM2018131]; L.M. acknowledges support from the European Union{\textquoteright}s Horizon 2020 Programme (H2020-INFRAIA-2018-1) [823839]; Research Founda- tion Flanders (FWO) [G032816N, G042518N, G028821N]; W.V. acknowledges support from the Research Foundation Flanders (FWO) [G032816N, G028821N]; A.R. acknowledges support from the Fondazione Cassa Di Risparmio di Firenze [24316]; European Commission [101017567]; M.H.C. acknowledges the AIRC project to MHC [IG 23539]; J.F.-R. acknowledges support from the Spanish Ministry of Science and Innovation [PID2019-110167RB-I00]; N.R. acknowledges support from the Norwegian Research Council (Norges Forskningsr{\aa}d) [288008]; E.D.L. acknowledges support from the European Union{\textquoteright}s Horizon 2020 research and innovation programme [819318]; M.J.E.S. acknowledges support from the Wellcome Trust [104955/Z/14/Z, 218242/Z/19/Z]. Funding for open access charge: Biotechnology and Biological Sciences Research Council grant [BB/T01959X/1]; Wellcome Trust [104955/Z/14/Z and 218242/Z/19/Z]. Conflict of interest statement. None declared. Publisher Copyright: {\textcopyright} The Author(s) 2021. Copyright: Copyright 2022 Elsevier B.V., All rights reserved.",

year = "2022",

month = jan,

day = "7",

doi = "10.1093/nar/gkab988",

language = "English",

volume = "50",

pages = "D534--D542",

journal = "Nucleic Acids Res",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "D1",

}

TY - JOUR

T1 - PDBe-KB: collaboratively defining the biological context of structural data

AU - PDBe-KB consortium

AU - Varadi, Mihaly

AU - Anyango, Stephen

AU - Armstrong, David

AU - Berrisford, John

AU - Choudhary, Preeti

AU - Deshpande, Mandar

AU - Nadzirin, Nurul

AU - Nair, Sreenath S.

AU - Pravda, Lukas

AU - Tanweer, Ahsan

AU - Al-Lazikani, Bissan

AU - Andreini, Claudia

AU - Barton, Geoffrey J.

AU - Bednar, David

AU - Berka, Karel

AU - Blundell, Tom

AU - Brock, Kelly P.

AU - Maria Carazo, Jose

AU - Damborsky, Jiri

AU - David, Alessia

AU - Dey, Sucharita

AU - Dunbrack, Roland

AU - Fernandez Recio, Juan

AU - Fraternali, Franca

AU - Gibson, Toby

AU - Helmer-Citterich, Manuela

AU - Hoksza, David

AU - Hopf, Thomas

AU - Jakubec, David

AU - Kannan, Natarajan

AU - Krivak, Radoslav

AU - Kumar, Manjeet

AU - Levy, Emmanuel D.

AU - London, Nir

AU - Macias, Jose Ramon

AU - Srivatsan, Madhusudhan M.

AU - Marks, Debora S.

AU - Martens, Lennart

AU - McGowan, Stuart A.

AU - McGreig, Jake E.

AU - Modi, Vivek

AU - Gonzalo Parra, R.

AU - Pepe, Gerardo

AU - Piovesan, Damiano

AU - Prilusky, Jaime

AU - Putignano, Valeria

AU - Radusky, Leandro G.

AU - Ramasamy, Pathmanaban

AU - Rausch, Atilio O.

AU - Vranken, Wim

N1 - Funding Information: ELIXIR [IDP implementation study]; Biotechnology and Biological Sciences Research Council via the 3D-Gateway [BB/T01959X/1]; FunPDBe [BB/P024351/1]; European Molecular Biology Laboratory-European Bioinformatics Institute who supported this work; J.D. acknowledges support from the Ministry of Education, Youth and Sport of the Czech Republic [INBIO CZ.02.1.01/0.0/0.0/16 026/0008451]; R.S., K.B. and J.D. also acknowledge support from the Ministry of Education, Youth and Sport of the Czech Republic [ELIXIR-CZ LM2018131]; L.M. acknowledges support from the European Union’s Horizon 2020 Programme (H2020-INFRAIA-2018-1) [823839]; Research Founda- tion Flanders (FWO) [G032816N, G042518N, G028821N]; W.V. acknowledges support from the Research Foundation Flanders (FWO) [G032816N, G028821N]; A.R. acknowledges support from the Fondazione Cassa Di Risparmio di Firenze [24316]; European Commission [101017567]; M.H.C. acknowledges the AIRC project to MHC [IG 23539]; J.F.-R. acknowledges support from the Spanish Ministry of Science and Innovation [PID2019-110167RB-I00]; N.R. acknowledges support from the Norwegian Research Council (Norges Forskningsråd) [288008]; E.D.L. acknowledges support from the European Union’s Horizon 2020 research and innovation programme [819318]; M.J.E.S. acknowledges support from the Wellcome Trust [104955/Z/14/Z, 218242/Z/19/Z]. Funding for open access charge: Biotechnology and Biological Sciences Research Council grant [BB/T01959X/1]; Wellcome Trust [104955/Z/14/Z and 218242/Z/19/Z]. Conflict of interest statement. None declared. Publisher Copyright: © The Author(s) 2021. Copyright: Copyright 2022 Elsevier B.V., All rights reserved.

PY - 2022/1/7

Y1 - 2022/1/7

N2 - The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.

AB - The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.

UR - http://www.scopus.com/inward/record.url?scp=85125170185&partnerID=8YFLogxK

U2 - 10.1093/nar/gkab988

DO - 10.1093/nar/gkab988

M3 - Article

VL - 50

SP - D534-D542

JO - Nucleic Acids Res

JF - Nucleic Acids Res

SN - 0305-1048

IS - D1

ER -

PDBe-KB: collaboratively defining the biological context of structural data

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this